Array-based method for performing genomic analysis

Abstract

An array-based method for performing genomic analysis is provided. In certain embodiments, the method may comprise: a) contacting a sample comprising genomic DNA with a Type IIB restriction enzyme to produce Type IIB fragments; b) directly labeling the Type IIB fragments with a fluorescent label to produce labeled fragments; c) contacting the labeled fragments with an array to produce a contacted array; and d) reading the contacted array to produce data. In certain instances, the data may be analyzed to determine the copy number of a genomic region in the sample. Also provided are arrays and kits useful to practice the method.

1 . A method of sample analysis, comprising:
 a) contacting a sample comprising genomic DNA with a Type IIB restriction enzyme to produce Type IIB fragments;   b) directly labeling said Type IIB fragments with a fluorescent label to produce labeled fragments;   c) contacting said labeled fragments with an array under suitable hybridization conditions to produce a contacted array;   d) reading said contacted array to provide data.   
     
     
         2 . The method of  claim 1 , wherein said directly labeling comprises adding a single fluorescently labeled dideoxynucleotide to said Type IIB fragments using a terminal transferase to produce single nucleotide extended Type IIB fragments. 
     
     
         3 . The method of  claim 2 , wherein said array comprises oligonucleotide probes that are complementary to said terminally extended Type IIB fragments, including said single nucleotide. 
     
     
         4 . The method of  claim 3 , wherein said oligonucleotide probes comprise a hairpin comprising a terminal nucleotide that is adjacent to said single nucleotide, when said single nucleotide extended Type IIB fragments are hybridized to said oligonucleotide probe. 
     
     
         5 . The method of  claim 1 , wherein said Type IIB fragments are not amplified prior to said directly labeling. 
     
     
         6 . The method of  claim 1 , further comprising: e) analyzing said data to provide an absolute copy number of a genomic locus. 
     
     
         7 . The method of  claim 6 , wherein said data is not compared to data obtained using a reference sample. 
     
     
         8 . The method of  claim 1 , wherein said contacting step a) produces Type IIB fragments, and said method comprises size separating said Type IIB fragments from the remainder of said genome prior to said directly labeling step b). 
     
     
         9 . The method of  claim 8 , wherein said size separating is done by gel electrophoresis or column chromatography. 
     
     
         10 . The method of  claim 1 , wherein said genomic DNA is suspected of having a copy number abnormality. 
     
     
         11 . The method of  claim 1 , wherein said sample comprises 1-20 μg of mammalian genomic DNA. 
     
     
         12 . The method of  claim 1 , wherein said contacting step a) employs more than one Type IIB restriction enzyme. 
     
     
         13 . The method of  claim 1 , wherein contacting step c) is done under conditions that provide for binding equilibrium. 
     
     
         14 . An oligonucleotide array comprising a plurality of features each comprising a surface-tethered oligonucleotide that has a region complementary to a part of the sequence of a single nucleotide extended Type IIB fragment, said part including the extended nucleotide. 
     
     
         15 . The oligonucleotide array of  claim 14 , wherein said features comprise surface-tethered oligonucleotides having a region complementary to the entire sequence of a single nucleotide extended Type IIB fragment. 
     
     
         16 . The oligonucleotide array of  claim 14 , wherein said features comprise surface-tethered oligonucleotides that are T m  matched. 
     
     
         17 . The oligonucleotide array of  claim 14 , wherein said surface-tethered oligonucleotide further comprises a hairpin structure that terminates adjacent to the extended nucleotide of a single nucleotide extended Type IIB fragment. 
     
     
         18 . The oligonucleotide array of  claim 17 , wherein said hairpin structure provides for stacking of the Type IIB fragment, when said Type IIB fragment is hybridized to said surface-tethered oligonucleotide. 
     
     
         19 . The oligonucleotide array of  claim 14 , wherein said surface-tethered oligonucleotide is in the range of 27 to 100 nucleotides in length. 
     
     
         20 . A kit for performing an array analysis on a sample of genomic DNA comprising:
 a) an oligonucleotide array comprising surface tethered oligonucleotides that are complementary to Type IIB restriction enzyme fragments;   b) a Type IIB restriction enzyme;   c) reagents for directly labeling said Type IIB fragments by adding a single fluorescent nucleotide to a terminus to produce labeled fragments; and   e) reagents for hybridizing said of the labeled fragments to said array.   
     
     
         21 . The kit of  claim 19 , wherein said reagents for directly labeling comprise a terminal transferase.